Compiler generated systolic arrays for wavefront algorithm acceleration on FPGAs

Betul Buyukkurt, Walid A. Najj
2008 2008 International Conference on Field Programmable Logic and Applications  
Wavefront algorithms, such as the Smith-Waterman algorithm, are commonly used in bioinformatics for exact local and global sequence alignment. These algorithms are highly computationally intensive and are therefore excellent candidates for FPGA-based code acceleration. However, there is no standard form of these algorithms, they are used in a wide variety of situations with various constraints. It is therefore not practical to have a standard kernel that can be mapped to an FPGA, hence the
more » ... tance of being able to compile such codes from a high level language. ROCCC is a C to VHDL compiler, which optimizes and parallelizes the most frequently executed kernel loops in applications such as in multimedia, scientific and high-performance computing. In this paper we describe the transformations performed by ROCCC, which transformed the kernel of the Smith-Waterman algorithm into a hardware systolic array that is mapped onto the FPGA on the SGI Altix RASC blade. We report a throughput increase by over 3,000X over a 2.8 GHz Xeon.
doi:10.1109/fpl.2008.4630032 dblp:conf/fpl/BuyukkurtN08 fatcat:qas2izyfljcn7kfv2oa5z6hwia